A script to convert pombase gff3 file into GFT format compatible with transvar.
You need to have docker installed. Then simply run: bash run_with_docker.sh
The output gtf file will be at data/pombase_genome.gtf
.
What it does:
get_data.sh
).scripts/pombasegtf_to_ensemblgtf.py
.Install python dependencies and activate virtual env:
poetry install
poetry shell
See the file run_locally.sh
, which downloads and installs several dependencies if not present:
samtools
htslib
You can install them with brew or apt otherwise
# If you have linux and you want to install them globally
sudo apt install -y samtools tabix gffread
# Installing globally in mac
brew install htslib samtools gffread
Then runs bioconvert as well as the python script.